title: PCSK9 is involved in human induced pluripotent stem cell proliferation through the regulation of the NODAL signaling pathway

city: Nantes

first: Antoine

last: Rimbert

address: 8 quai moncousu

institute: Institut du thorax inserm-U1087

summary: Proprotein convertase subtilisin kexin type 9 (PCSK9) is a key regulator of LDL cholesterol metabolism and the target of lipid-lowering drugs. PCSK9 is mainly expressed in hepatocyte. Here, we show that PCSK9 is highly expressed in undifferentiated hiPSCs. PCSK9 inhibition in hiPSCs with the use of shRNA, CRISPR/cas9-mediated knockout or endogenous PCSK9 loss-of-function mutation R104C/V114A unveiled its new role as a potential cell cycle regulator through the NODAL signaling pathway. Indeed, PCSK9 inhibition leads to a decrease of SMAD2 phosphorylation and hiPSCs proliferation. Conversely, PCSK9 overexpression stimulates hiPSCs proliferation. PCSK9 can interfere with the NODAL pathway by regulating the expression of its endogenous inhibitor DACT2, which is involved in the TGFß-R1 lysosomal degradation. Using different PCSK9 constructs we show that PCSK9 interacts with DACT2 through its CHRD domain. Altogether these data highlight a new role of PCSK9 in cellular proliferation and development, beyond its canonical effect on lipid metabolism.

overall_design: PCSK9 has been either: knocked out using CRISPR-Cas9 gene edition system (PCSK9-ko; N=12) or overexpressed (PCSK9-overexpression; N=3) in induced pluripotent stem cells. PCSK9 knockout in control hiPS cells was generated using the Alt-R™ CRISPR-Cas9 System (Integrated DNA Technologies) targeting the exon 7 of PCSK9 at both alleles. Briefly gRNA CCAGCGACTGCAGCACCTGC was first duplexed with the Alt-R® CRISPR-Cas9 tracrRNA, then complexed to the Alt-R® S.p. Cas9 Nuclease according to IDT recommandations. Full length PCSK9 overexpression has been obtained by specific insertion at the AAVS1 site with plasmids encoding for hAAVS1 1R TALEN (Addgene #35432) and hAAVS1 1L TALEN (Addgene #35431) homologous sequences. Thereafter, hiPSCs were selected with Puromycin (TOCRIS Bioscience 4089/50; up to 8µg/ml) and  verified by PCR sequencing

first: Karim

last: Si-Tayeb


title: The FimZ regulon of E. coli in the stationary phase

status: Public on Aug 05 2021

city: Koganei

first: Kaneyoshi

last: Yamamoto

state: Tokyo

address: 3-7-2 Kajinocho

department: Frontier Bioscience

country: Japan

institute: Hosei University

summary: To compare the transcriptional profiling of a FimZ-expressing strain or non-expressing strain in E. coli under stationary phase. For overexpression of fimZ gene was cloned into pBAD33 plasmid under control of the arabinose-inducible PBAD promoter, which was induced by addition of 0.2% arabinose. Goal was to determine the FimZ regulon in E. coli. Biological replicates: 2 replicates.

platform_organism: Escherichia coli str. K-12 substr. MG1655

first: Yuki

last: Yamanaka


title: 2-Phenylmaltol treatment induces cytotoxicity in human cancer cell lines.

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: Gene expression anlysis of  2-Phenylmaltol terted HeLa and HCT116 cells.

overall_design: After treated with 2-Phenylmaltol for 48 hours, RNA was extracted from trerted cells and cDNA was synthesized , and then the change in gene expression was analyzed by 3D gene microarray analysis.

first: Takahito

last: Ohira

first: Hiroyuki

last: Kugoh


title: Cardiorespiratory Fitness in Children with Overweight-Obesity: Insights into the Molecular Mechanisms

city: Irvine

first: ABEL

last: PLAZA FLORIDO

state: California

address: 101 Academy, Suite 150 Irvine

department: Department of Pediatrics, UC Irvine School of Medicine

country: USA

institute: Pediatric Exercise and Genomics Research Center (PERC)

type: Expression profiling by high throughput sequencing

summary:
This study aimed to analyze the whole-blood transcriptome profile of fit children with overweight/obesity (OW/OB) compared to unfit children with OW/OB.
Methods: 27 children with OW/OB (10.14 ± 1.3 years, 59% boys) from the ActiveBrains project were evaluated. VO2peak was assessed using a gas analyzer, and participants were categorized into fit or unfit according to the CVD risk-related cut-points. Whole-blood transcriptome profile (RNA sequencing) was analyzed. Differential gene expression analysis was performed using Limma R/Bioconductor software package (analyses adjusted by sex and maturational status).
Results: 256 genes were differentially expressed in fit children with OW/OB compared to unfit children with OW/OB after adjusting by sex and maturational status (FDR < 0.05). Enriched pathways analysis identified gene pathways related to inflammation (e.g., dopaminergic and GABAergic synapse pathways).
Conclusion: The distinct pattern of whole-blood gene expression in fit children with OW/OB reveals genes and gene pathways that might play a role in reducing CVD risk factors later in life.

overall_design: Total whole blood mRNA profiles of 27 children with overweight/obesity were analyzed by 5’-end RNA sequencing. Cardiorespiratory fitness (i.e., VO2peak) was quantified using a gas analyzer (General Electric Corporation) while performing a maximal incremental treadmill test (HP-Cosmos ergometer). The maturational status of the participants was reflected by peak height velocity (PHV) using age and height in validated algorithms (Moore et al. 2015; PMID: 25423445).

first: Abel

last: Plaza-Florido

first: Signe

last: Altmäe

first: Francisco

middle: J

last: Esteban

first: Marie

last: Löf

first: Shlomit

last: Radom-Aizik

middle: B

last: Ortega Porcel


title: Bulk RNAseq for hiPS-CMs induced to proliferate with 4 cell cycle factors

city: Louisville

first: Tamer

middle: M

last: Mohamed

state: KY

address: 580 S. Preston St., Baxter II Bldg., Room 122

department: Cardiology

institute: University of Louisville

summary: we conducted temporal bulk RNAseq on 60-day-old mature hiPS-CMs infected with either LacZ (control) or CDK1, CDK4, CCNB, CCND (4F) adenovirus for 24, 48 or 72 h.

first: Riham

middle: R

last: Abouleisa


title: Transcriptional dissection of lateral root primordium cells

city: Pozuelo de Alarcon

first: Miguel

middle: Angel

last: Moreno-Risueno

state: Madrid

department: Biotechnology

country: Spain

institute: Center for Plant Biotechnology and Genomics

summary: To specifically profile early stages of lateral root formation we used the marker pHB53:NLS-3xmCherry, which is only expressed in lateral root primordium cells. We isolated ~2,000 lateral root primordium cells from stages I to IV through Fluorescent Activated Cell Sorting, and profiled the transcriptome of 573 of these cells. As a LR primordium has ~6-10 cells at stage I and ~30-40 cells at stage IV, the number of sequenced cells would approximately cover 5-6 fold the total number of cells in the stages profiled.

overall_design: Single-cell RNAseq of lateral root primordium cells at stages I-IV.

first: Alvaro

last: Sanchez-Corrionero

first: Kenneth

middle: D

last: Birnbaum

middle: A

first: Laura

last: Serrano-Ron

first: Pablo

last: Perez-Garcia


title: Transcriptome analysis of Upland Cotton revealed novel pathways to scavenge reactive oxygen species (ROS) responding to Na2SO4 tolerance

city: Anyang

first: Qinqin

last: Wang

state: HeNan

address: 38 Huanghe Avenue

country: China

institute: Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan 455000 China.

summary: To explore the mechanisms of cotton response to Na2SO4 stress, we used next-generation sequencing (NGS) technology to study transcriptional changes of cotton under the treatment of 300 mmol• L-1 Na2SO4 solution at 12 h and the control with water at 12 h. A total of 15,524, 20,409 and 12,146 differentially expressed genes (DEGs) were identified in cotton roots, stems and leaves between treatment and control, respectively. Gene ontology (GO) analysis indicated the enrichment of DEGs involved in various stimuli or stress responses. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that DEGs associated with plant hormone signal transduction, plant-pathogen interaction, and Starch and sucrose metabolites were regulated in response to the Na2SO4 stress. We further analyzed genes enriched in ROS (reactive oxygen species) scavenging system including osmotic stress and ion toxicity were significantly up-regulated. In addition, analysis for sulfur metabolism, results in to identification of two rate limiting enzymes APR and OASTL during synthesis of GSH from SO42-. The analysis of the expression profiles of diverse tissues under Na2SO4 stress and identification of relevant key hub genes in a network crosstalk will provide a strong foundation and valuable clues for genetic improvements of cotton in response to various salt stresses.

overall_design: The transcriptional levels of cotton was tested in cotton roots, stems and leaves between the treatment of 300 mmol• L-1 Na2SO4 solution at 12 h and the control with water at 12 h.

first: Wuwei

last: Ye


title: Identification of alternative splicing changes upon ablation of cytoplasmic SRSF1.

city: Edinburgh

first: Magdalena

middle: Maria

last: Maslon

address: Crewe Road

country: United Kingdom

institute: University of Edinburgh

summary: SRSF1, shuttles between the nucleus and cytoplasm affecting post-splicing processes. However, the physiological significance of this remains unclear. Here, we used genome editing to knock-in a nuclear retention signal (NRS) in Srsf1 to create a mouse model harboring a non-shuttling SRSF1 protein. We then assessed whether alblation of shuttling activities of SRSF1 affects its nuclear functions.

overall_design: Mouse fibroblasts were derived from wild type or homozygous or heterozygous SRSF1-NRS mice. Total RNA was isolated from MEFs and subject to sequencing. Alternative splicing analysis was performed using Suppa2. Three replicates for WT and homozygous MEFs, and 2 replicates for heterozygous MEFs were used.

first: Fiona

last: Haward

first: Patricia

middle: L

last: Yeyati

first: Nicolas

last: Bellora

first: Stuart

last: Aitken

first: Alex

last: von  Kreigsheim

first: Pleasantine

last: Mill

first: Ian

last: Adams

first: Javier

middle: F

last: Cáceres


title: Identification of polysomal-association changes upon ablation of cytoplasmic SRSF1

summary: SRSF1, shuttles between the nucleus and cytoplasm affecting post-splicing processes. However, the physiological significance of this remains unclear. Here, we used genome editing to knock-in a nuclear retention signal (NRS) in Srsf1 to create a mouse model harboring a non-shuttling SRSF1 protein. We then assessed how alblation of shuttling activities of SRSF1 affects mRNA translation.

overall_design: Sequencing of total, monosomal, polysomal RNA from ESC, MEF and NSC cells expressing wild type or nuclear retained SRSF1

last: von Kreigsheim


title: CLAMP and Zelda function together as pioneer transcription factors to promote Drosophila zygotic genome activation [ATAC-Seq]

city: Ithaca

first: Ellie

last: Duan

state: New York

address: 507 Tower Rd., Ithaca, NY 14853, Ithaca, NY 1485

department: Animal Science

institute: Cornell University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The pioneer transcription factor Zelda (ZLD) increases the accessibility of chromatin to promote the essential process of zygotic genome activation (ZGA) in the Drosophila early embryo. However, many genomic loci remain accessible in the absence of ZLD and are enriched for GA-rich DNA binding motifs. Therefore, we hypothesized that other pioneer TFs that function with ZLD have not yet been identified, especially those that bind to GA-rich motifs. CLAMP (Chromatin-linked adaptor for Male-specific lethal MSL proteins) is a GA-rich motif binding TF that is essential for early embryonic development. Here, we identify for the first time that CLAMP is a pioneer TF which interacts directly with nucleosomes, regulates zygotic genome activation, promotes chromatin accessibility, and facilitates the binding of ZLD to promoters. When ZLD is bound at a locus but does not regulate chromatin accessibility, CLAMP can often function redundantly to open the chromatin. Because ZGA is an essential process across metazoans, it is key to evolve redundant pioneer TFs to protect organisms from lethality that would be caused by loss of a single non-redundant factor.

overall_design: ATAC-seq was used to determine chromatin accessibility of 0-2hr and 2-4hr embryos that had maternal CLAMP depletion;

first: Duan

last: Ellie

first: Leila

middle: E

last: Rieder

first: Annie

last: Huang

first: W

middle: T

last: Jordan III

first: Mary

last: McKenney

first: Scott

last: Watters

last: Fawzi

first: Erica

last: Larschan


title: Yap/Taz regulates pericyte differentiation in the embryonic kidney

city: Dallas

first: Thomas

last: Carroll

address: 6000 Harry Hines Blvd.

institute: UT Southwestern

summary: The embryonic renal stroma is highly heterogeneous; however, the significance of this cellular diversity has been poorly understood. Here, we identify a subpopulation of embryonic stroma with enriched Yap/Taz signaling that functions in supporting the developing microvasculature, demonstrating that distinct stromal cells have unique roles in normal renal development.

overall_design: Mouse models with  deletion of the paralogs Yap and Taz in the stromal lineage were generated by crossing Foxd1cre transgenic with mice carrying loxP-flanked Yap (Yapflox/flox or Yapc/c) or Taz/Wwtr1 (Tazflox/flox or Tazc/c) alleles.

first: Keri

last: Drake


title: TonEBP-deficiency accelerates age-dependent intervertebral disc degeneration underscored by matrix remodeling, cytoskeletal rearrangements, and changes in proinflammatory gene expression

city: Philadelphia

first: Steven

last: Tessier

state: Pennsylvania

address: 3700 Gateway Dr., Apt 622

department: Orthopedic Surgery

institute: Thomas Jefferson

summary:
Our studies show that TonEBP-deficiency causes pronounced degeneration of all three intervertebral disc compartments with greater incidence of herniation in the mouse. The disc phenotype is marked by extracellular matrix remodeling, actin cytoskeleton rearrangements, and suppressed proinflammatory gene expression, advancing our understanding of the contributions of TonEBP in intervertebral disc homeostasis and disease.
We used microarray to explore the transcriptomics of differentially expressed genes of annulus fibrosus (AF) and nucleus pulposus (NP) tissue in TonEBP haploinsufficient mice on a C57BL/6 background.

overall_design: AF and NP tissue were dissected from lumbar discs (L1-S1) of 12-month-old TonEBP haploinsufficient and wild-type mice (n=3). RNA extraction and hybridization on Affymetrix microarrays.

first: Emanuel

last: Novais


title: DNA methylation profiling of circulatory monocytes in community-acquired pneumonia

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

type: Methylation profiling by high throughput sequencing

summary: In this study, we sought to broaden our understanding of circulatory monocyte functions captured during the acute (on hospital admission) and recovery (one-month follow-up) stages of patients diagnosed with community-acquired pneumonia (CAP).

overall_design: Examination of DNA methylation in circulating CD14+ monocytes obtained from CAP patients on hospital admission (CAP), from the same patients after one month recovery (CAPD28), and age, gender, and comorbidity-matched control participants (HV).

middle: P

first: Xanthe

last: Brands


title: DNA Methylation Profiling in Mummified Human Remains from the Eighteenth-Century

status: Public on Aug 04 2021

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

summary: Reconstruction of ancient epigenomes by DNA methylation (DNAm) can shed light into the composition of cell types, disease states, and age at death. However, such analysis is hampered by impaired DNA quality and little is known how decomposition affects DNAm. In this study, we determined if EPIC Illumina BeadChip technology is applicable for specimen from mummies of the 18th century CE. Overall, the signal intensity on the microarray was extremely low, but for one of two samples we detected characteristic DNAm signals in a subset of CG dinucleotides (CpGs), which were selected with a stringent processing pipeline. Using only these CpGs we could train epigenetic signatures with reference DNAm profiles of multiple tissues and our predictions were in line with the fact that the specimen was lung tissue of a female 28-year-old donor. Thus, we provide proof of principle that Illumina BeadChips are applicable for DNAm profiling in ancient samples.

overall_design: Bisulphite converted DNA of two different mummies of the 18th century was hybridised to the Illumina Infinium EPIC Human Methylation Beadchip.

first: Marco

last: Schmidt

first: Frank

last: Maixner

first: Gerhard

last: Hotz

first: Ildikó

last: Pap

first: György

last: Pálfi

first: Ildiko

last: Szikossy

first: Albert

last: Zink


title: Genome-wide DNA methylome analysis identifies putative biomarkers associated with the survival of human ovarian cancers [30 cases]

status: Public on Aug 11 2021

city: Pokfulam

first: David

middle: Wai

last: Chan

state: Hong Kong

address: L747 Laboratory Block, LKS Faculty of Medicine, 21 Sassoon Road

department: Obs. & Gyn.

country: Hong Kong

institute: The Uniersity of Hong Kong

type: Methylation profiling by genome tiling array

summary: We conducted an epigenome-wide association study (EWAS) to evaluate global DNA methylation in EOC. In a retrospective cohort of 30 HGSOC subtype primary ovarian cancers, we observed that global DNA hypermethylation was preferentially associated with recurrent HGSOC. A total of 2,969 DMPs corresponding to 1,471 genes were involved in olfactory transduction, and calcium and cAMP signaling.

overall_design:
Whole-genome DNA methylation analysis was performed on a retrospective cohort of 30 HGSOC patients with platinum-sensitive and platinum-resistant samples.
contributor: Centre for PanorOmic Sciences (CPOS), Genomics Core, HKU


title: Genotyping data from 49 patient with unexplained mental retardation

city: Hidaka

first: Masakazu

last: KOHDA

state: Saitama

address: 1397-1 Yamane

institute: Saitama Medical University

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary: In the study we present a multicenter study in which three European diagnostic centres assessed the use of Affymetrix Mapping 500k SNP arrays for molecular karyotyping in patients with mental retardation. Each centre tested DNA from 40 patients with unexplained mental retardation together with their parents. In addition, 38 DNA samples containing known submicroscopic copy number variations (CNVs) were run for validation purposes.

overall_design: We performed a validation experiment where genomic DNA of 49 patients with mental retardation was hybridized onto Affymetrix' GeneChip 6.0 SNP  arrays, and identified genome-wide CNVs.


title: Differential DNA Methylation and Transcriptional Signatures Characterize Impairment of Progenitor Cells in Pediatric Human Muscle Contractures Following Brain Injury [RNA-seq]

city: Chicago

first: Andrea

middle: A.

last: Domenighetti

state: IL

address: 345 East Superior St

institute: Northwestern University & Rehabilitation Institute of Chicago

summary: Limb contractures are a debilitating and progressive consequence of a wide range of pediatric conditions that affect skeletal muscles, including perinatal brain injury causing cerebral palsy (CP). While several rehabilitation therapies are currently used in the clinical setting, their long-term effectiveness in treating contractures is marginal since they do not change underlying muscle biological properties. Therefore, new therapies based on a biological understanding of contracture development are needed. Here we show that myoblast progenitor cells from contractured muscle in children with CP had higher rates of proliferation than control cells from typically developing children. This phenotype was associated with upregulation of DNMT3a and patterns of DNA hypermethylation and gene expression that favored cell expansion over quiescence. Treatment of CP progenitors with 5-azacytidine, a DNMT inhibitor and hypomethylating agent, normalized this epigenetic imprint and promoted exit from mitosis. Together with previous studies demonstrating reduction in myoblast differentiation capacity, these data suggest that mechanisms of early myofiber growth and establishment of an adult population of quiescent stem cells could be compromised in CP. Hypomethylating agents like 5-azacytidine could be used to rescue myogenesis and promote muscle growth in contractured muscle and thus may represent a new approach to treating this devastating condition

overall_design: We performed RNA sequencing analysis of dividing satellite cell-derived myoblast precursors from contractured cerebral palsy (CP) muscles and typically developing (TD) control muscles, treated and non-treated with hypomethylating agent 5-azacytidine (AZA)


title: Differential DNA Methylation and Transcriptional Signatures Characterize Impairment of Progenitor Cells in Pediatric Human Muscle Contractures Following Brain Injury

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: DNA Methylation Alterations in Blood Cells of Toddlers with Down Syndrome

city: Houston

first: Oxana

middle: Yu.

last: Naumova

state: TX

address: 4849 Calhoun Rd, TIMES, Rm 373

department: Psychology

institute: University of Houston

summary: Genome-wide DNA methylation profiling of whole blood cells. The Illumina Infinium HumanMethylation450 microarray was used. Two children's cohorts were studied: 17 children with Down syndrome (DS) and 17 typically developing children (TD)

overall_design: Bisulphite converted DNA from the 34 samples were hybridized to the Illumina Infinium HumanMethylation450 Beadchip.

middle: Y

first: Elena

last: Grigorenko


title: Two auxinic herbicides alter Brassica napus changes in transcription in a time dependent manner

city: Dresden

first: Jutta

last: Ludwig-Müller

address: Zellescher Weg 20b

department: Biology

institute: Technische Universität Dresden

summary: The aim of this study was to investigate the molecular background by using different growth conditions under which three different auxinic herbicides were administered. These were halauxifen-methyl, and picloram at thre different harvest points after treatments (2, 48, 96 hours). Hal treatment lead to the upregulation of translational processes after 2 h, whereas auxin and hormone responses were upregulated at 48h and 96 h. Photosynthesis and mitochondrial pro-cesses were downregulated through all time points. Further, after 48 h translation was downreg-ulated. Pic treatment induced the hormone / auxin response already after 2 h, and this continued for the other time points. At 2 h and 48 h after treatment the translational processes were down-regulated and photosynthesis was downregulated after 48 h and 96 h. The more detailed analy-sis of the auxin response in the datasets indicate a role for GH3 genes, genes encoding auxin efflux proteins and confirm the upregulation of the ethylene pathway.

overall_design: The treatments with the auxinic herbicides halauxifen-methyl and picloram were performed at 15°C and growth stage BBCH11 (4 leaves) by pipetting the working solution onto the leaves taking care that these did not roll from the leaves. Each plant got 5 drops per treatment with a total herbicide concentration of 0.5 µg/µl Halauxifen and 2.4 µg/µl picloram. controls were treated with the solvent (1% DMSO, 0.01% Triton X-100, 0.01M NaOH). The harvest was done 2, 48 and 96 hours after application. For each treatment 3 replicates were performed.

first: Jörg

last: Becker

first: Agnes

last: Rost


title: Cellular transcriptomes of wild-type and ING3 knockout HT-29 cells

city: St. Louis

first: Gaopeng

last: Hou

state: MO

address: McDonnell Pediatric Research Building, Rm 9220

department: molecular microbiology

institute: Washinton University inSt. Louis

summary: The goal of this study is to use RNA-sequencing to profile the transcriptional changes in HT-29 cells with ING3 deficiency. Specifically, we were interested in determining the IFN and ISGs in response to ING3 KO. Several ISGs including IFI44L and IFITM1 were up-regulated in ING3 KO HT-29 cells, indicating that the broad resistance to virus infection in ING3 KO cells were mediated by heightened IFN and ISG responses.

overall_design:
mRNA profiles of WT and ING3 KO HT-29 cells were analyzed by bulk RNA-sequencing
We used one sgRNA to knockout ING3 in HT-29 cells, then we subcloned the HT-29-ING3 KO cells. #1 and #2 mean different subclones of HT-29-ING3 KO cells.

first: Y

last: Song

first: S

last: Ding


title: Detecting disease patterns using early-stage patient derived induced pluripotent stem cells

city: Kyoto

first: Ying

last: Chen

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

institute: Center for iPS Cell Research and Application, Kyoto University

summary: We reported the application of 21 human induced pluripotent stem cells and 2 human embryonic stem cells to establish a perdiciton model for disease affected tissues

overall_design: RNA sequencing for 23 undifferentiated stem cell lines.

first: Kenta

last: Kobayashi

first: Junko

last: Yamane


title: RiboDoc: a Docker-based package for ribosome profiling analysis

city: Orsay

first: Olivier

last: Namy

address: Rue Gregor Mendel, bat 400

country: France

institute: CNRS, Université Paris-Sud

summary: Ribosome profiling (RiboSeq) has emerged as a powerful technique for studying the genome-wide regulation of translation in various cells. Several steps in the biological protocol have been improved, but the bioinformatics part of RiboSeq suffers from a lack of standardization, preventing the straightforward and complete reproduction of published results. Too many published studies provide insufficient detail about the bioinformatics pipeline used. The broad range of questions that can be asked with RiboSeq makes it difficult to use a single bioinformatics tool. Indeed, many scripts have been published for addressing diverse questions. Here, we propose a unique tool (for use with multiple operating systems, OS) to standardize the general steps that must be performed systematically in RiboSeq analysis, together with the statistical analysis and quality control of the sample. The data generated can then be exploited with more specific tools. We hope that this tool will help to standardize bioinformatics analyses pipelines in the field of translation.

overall_design: comparison between a WT yeast strain and a strain in which the frameshiffted  OAZ1 gene has been replaced by an in-frame version of OAZ1

first: Pauline

last: François

first: Hugo

last: Arbes

first: Stéphane

last: Demais

first: Agnès

last: Baudin-Baillieu


title: Differentially expressed genes in myotubes derived from MBNL knockouts hiPSCs generated by CRISPR/Cas9.

city: Corbeil-Essonnes

first: Hélène

last: Polvèche

address: 28, Rue Henri Desbruères

institute: I-Stem

summary: Alternative splicing has emerged as a fundamental mechanism not only for the diversification of protein isoforms but also for the spatiotemporal control of development. Therefore, a better understanding of how this mechanism is regulated has the potential not only to elucidate fundamental biological principles, but also to decipher pathological mechanisms implicated in diseases where normal splicing networks are misregulated. Here, we took advantage of human pluripotent stem cells to decipher during human myogenesis the role of MBNL proteins, a family of tissue-specific splicing regulators whose loss of function is associated with Myotonic Dystrophy type 1, an inherited neuromuscular disease. Thanks to the CRISPR/Cas9 technology, we generated human-induced pluripotent stem cells (hiPSCs) depleted in MBNL proteins and evaluated the molecular and functional consequences of this loss on the generation of skeletal muscle cells. Our results indicated that MBNL proteins are specifically required for the late myogenic maturation but not for early myogenic commitment. By a transcriptomic analysis, we further demonstrated that MBNL proteins are not only important for the regulation of alternative splicing but also for the regulation of gene expression. Together, our study reveals the temporal requirement of MBNL proteins in human myogenesis and should facilitate the identification of new therapeutic strategies capable to cope the loss of function of these MBNL proteins.

overall_design: 12 samples were analyzed with 3 replicates per condition: 3 WT hiPSC-derived myotubes (control), 3 DM1 hiPSC-derived myotubes, 3 MBNL1(-/-) hiPSC-derived myotubes and 3 MBNL1(-/-); MBNL2(-/-) DKO hiPSC-derived myotubes.

first: Antoine

last: Mérien

first: Cécile

last: Martinat

first: Margot

last: Jarrige


title: CLAMP and Zelda function together as pioneer transcription factors to promote Drosophila zygotic genome activation [ChIP-Seq]

first: Ellie

last: Duan

overall_design: ChIP-seq was used to measure CLAMP and ZLD occupancy to genome after clamp-i or zld-I in 0-2hr and 2-4hr embryos.

first: Duan

middle: J

last: Ellie

first: Leila

last: Rieder

first: Annie

last: Huang

first: W

last: Jordan III

first: Mary

last: McKenney

first: Scott

last: Watters

first: Nicolas

last: Fawzi

first: Erica

last: Larschan


title: Cell fusion enhances energy metabolism of mesenchymal tumor hybrid cells to sustain their proliferation and invasion

city: Toulouse

first: Frédéric

last: Chibon

address: 2 avenue Hubert Curien

department: Team 19 - INSERM UMR1037

institute: Cancer Research Center of Toulouse

summary: Cell-to-cell fusion is emerging as a key element of the metastatic process in various cancer types. We recently showed that hybrids made from the spontaneous merging of pre-malignant (IMR90 E6E7, i.e. E6E7) and malignant (IMR90 E6E7 RST, i.e. RST) mesenchymal cells recapitulate the main features of human undifferentiated pleomorphic sarcoma (UPS), with a highly rearranged genome and increased spreading capacities. To better characterize the intrinsic properties of these hybrids, we investigated here their metabolic energy profile compared to their parents. Our results unveiled that hybrids harbored a Warburg-like metabolism, like their RST counterparts. However, hybrids displayed a much greater metabolic activity, enhancing glycolysis to proliferate. Interestingly, modifying the metabolic environmental conditions through the use of 5-aminoimidazole-4-carbox-amide-1-β-D-ribofuranoside (AICAR), an activator of the 5’-adenosine monophosphate (AMP)-activated protein kinase (AMPK), specifically reduced the growth of hybrids, and also abrogated the invasive capacity of hybrids displaying enhanced glycolysis. Furthermore, AICAR efficiently blocked the tumoral features related to the aggressiveness of human UPS cell lines. Altogether, our findings strongly suggest that hybrids rely on higher energy flux to proliferate and that a drug altering this metabolic equilibrium could impair their survival and be potentially considered as a novel therapeutic strategy.

overall_design: Spontaneous in-vitro hybrid cells between transformed and immortalized fibroblasts

first: Ariadna

last: Brito

first: Candice

last: Merle

first: Pauline

last: Lagarde

first: Benjamin

last: Faustin

first: Anne

last: Devin

first: Lydia

last: Lartigue

first: Frederic


title: Differential gene expression analysis on forebrain,midbrain and hindbrain tissues dissected from 3 biological replicates of  P-25 wild type and Fmr1CRE knockin mutant mice

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

institute: University of Edinburgh, The Institute of Genetics and Cancer

summary: RNA Sequencing analysis was performed on RNA isolated from tissues(forebrain,midbrain and hindbrain) from P-25 wild type and Fmr1CRE knockin mutant mice from same litter.Random primed cDNA from poly(A) selected RNA was converted into an Illumina sequencing library using RNA Library Prep Kit from  Illumina (E7420, NEB, USA) in conjunction with NEBNext® Multiplex Oligos for Illumina (E7335/E7500, NEB, USA). and single-end 50-base pair (bp) reads were generated using a NextSeq 500 (Illumina Inc, SY-415-1002). Eighteen libraries were combined in two equimolar pools of 9 based on the library quantification results and each pool was run across a single High-Output Flow Cell. Sequencing was performed at the Wellcome Trust Clinical Research Facility (WTCRF; Edinburgh).  Fastq files were processed to transcript-level counts and quality control performed using the bcbio_nextgen pipeline and the illumina-RNAseq workflow template. Differential Expression (DE) analysis was performed in R. The R package bcbio-RNAseq was used to import salmon transcript level counts into DESeq2.

overall_design: 18 samples , with 6 groups(2 genotype and 3 samples each genotype) and 3 replicates per group.

first: Hemant

last: Bengani


title: Divergent and overlapping hippocampal and cerebellar transcriptome responses following  developmental ethanol exposure during the secondary neurogenic period.

city: Bryan

first: Rajesh

last: Miranda

state: Texas

address: 8441 Riverside Pkwy

department: Neuroscience and Experimental Therapeutics

institute: Texas A&M University School of Medicine

summary:
Purpose: Fetal alcohol spectrum disorders (FASD) result from ethanol exposure to the developing fetus. FASD occur in up to 1-5% of live births in the United States and there currently is no cure. Ethanol exposure to the developing central nervous system (CNS) has profound effects on learning and memory, impulse control, and motor function, resulting from neuropathology. The purpose of the current study was to perform transcriptome analysis to evaluate the effects of early postnatal ethanol exposure in the hippocampus and cerebellum.
Methods: Postnatal C57BL/6 mice were treated with 4g/kg of ethanol from P4-P9, brains were harvested 24h after the final treatment at P10, hippocampi and cerebella were microdissected, RNA was isolated, and RNASeq analysis was performed. We compared differences in gene expression, sex-dependent expression, and global biological pathways associated with disruptions in hippocampal and cerebellar genes between the ethanol and vehicle treated neonates.
Results: Ethanol caused both an up and down regulation of genes associated with the hippocampus and cerebellum, which may result in the disruption of normal circuitry and maturation and growth in these brain regions. Ethanol increased the expression of genes associated with the S phase of the cell cycle in both the hippocampus and cerebellum. In the cerebellum, ethanol increased effector gene expression, and in the hippocampus, genes associated with different interneuron lineages were altered. Postnatal ethanol exposure also resulted in altered expression of genes associated with oligodendrocyte lineages and myelination, along with alterations in microglia associated genes.
Conclusion: Collectively, these data indicate that ethanol has profound effects on the hippocampus and cerebellum, resulting in alterations of gene expression and biological pathways regulating neurodevelopment. These studies may have important implications concerning alcohol-induced neuropathology and the neurological effects seen across the life span in FASD.

first: Marisa

last: Pinson

first: James

middle: C

last: Douglas

first: Kalee

middle: N

last: Holloway

first: Paul

last: Drew


title: Tepoxalin increases chemotherapy efficacy in drug-resistant breast cancer cells overexpressing the multidrug transporter gene ABCB1

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

summary: Efficacious cancer chemotherapeutic treatment requires both therapy delivery and retention by malignant cells. Cancer cell overexpression of the multidrug transmembrane transporter gene ABCB1 thwarts therapy retention, leading to a drug-resistant phenotype. We explored the phenotypic impact of ABCB1 overexpression in normal human mammary epithelial cells (HMECs) via acute adenoviral delivery and in breast cancer cell lines with stable integration of inducible ABCB1 expression. One hundred sixty-two genes were differentially expressed between ABCB1-expressing and GFP-expressing HMECs, including the gene encoding the cyclooxygenase-2 protein, PTGS2. Several breast cancer cell lines with inducible ABCB1 expression demonstrated sensitivity to the 5-lipoxygenase, cyclooxygenase-1/2 inhibitor tepoxalin in two-dimensional drug response assays, and combination treatment of tepoxalin either with chemotherapies or with histone deacetylase (HDAC) inhibitors improved therapeutic efficacy in these lines. Moreover, selection for the ABCB1-expressing cell population was reduced in three-dimensional co-cultures of ABCB1-expressing and GFP-expressing cells when chemotherapy was given in combination with tepoxalin. Further study is warranted to ascertain the clinical potential of tepoxalin, an FDA-approved therapeutic for use in domesticated mammals, to restore chemosensitivity and improve drug response in patients with ABCB1-overexpressing drug-resistant breast cancers.

overall_design:
Human mammary epithelial cells (HMECs) were obtained from breast reduction surgery.  Cells were starved for 36 hours, and then infected with adenovirus expressing GFP or ABCB1 at an multiplicity of infection of 50 for 12 hours before RNA was collected.  Four replicates were used for each gene.
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Authors state "We are not allowed by IRB to release the raw data."

first: Jasmine

last: McQuerry

first: Jinfeng

last: Chen

first: Andrea

middle: H

last: Bild


title: Differentially expressed genes in myotubes derived from MBNL knockouts hiPSCs generated by CRISPR/Cas9

first: Hélène

last: Polvèche

overall_design: 9 samples were analyzed with 3 replicates per condition: 3 WT hiPSC-derived myotubes (control), 3 MBNL1(-/-) hiPSC-derived myotubes and 3 MBNL1(-/-); MBNL2(-/-) DKO hiPSC-derived myotubes.

first: Antoine

last: Mérien

first: Cécile

last: Martinat

first: Margot

last: Jarrige


title: Treatment with nanoliposomes loaded with ITE and MOG(35-55) ameliorates EAE

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

summary: To evaluate the therapeutic potential of NLP(ITE+MOG) in a mouse model of secondary progressive multiple sclerosis, we induced EAE in NOD mice and initiated weekly treatment with nanoliposomes beginning at 35 days post immunization during the chronic phase of disease. NLP(ITE+MOG) administration ameliorated EAE, and the transcriptional analysis of CNS-resident astrocytes, microglia and monocytes revealed decreased expression of genes associated with pro-inflammatory responses and neurodegeneration.

overall_design: Astrocytes, microglia and monocytes were isolated from the brains and spinal cords of mice with NOD EAE. Mice were treated with NLP (ITE+MOG) once weekly beginning at 35 days post immunization or left untreated as control.

first: Jessica

last: Kenison-White

first: Francisco

last: Quintana


title: RNA sequencing of zebrafish asxl1+/+ and asxl1-/-

city: Guangzhou

first: Xiao

last: Fang

state: Guangdong

address: Guangzhou Higher Education Mega Centre, Panyu District

department: School of Medicine

institute: South China University of Technology

summary: ASXL1 gene is one of the most frequently mutated genes in malignant myeloid diseases. In patients, ASXL1 mutations are usually heterozygous frameshift or non-sense mutations leading to C-terminal truncation. Here, we generated an endogenous C-terminal truncated Asxl1 mutant in zebrafish which is more comparable to human malignant leukemia patients. Our data showed that at embryonic stage, neutrophil differentiation was explicitly blocked in our mutant. To understand the basis for the impairment of neutrophil differentiation in zebrafish asxl1 mutants, we performed RNA-seq of asxl1 mutants at 3dpf and their littermate controls. Similar with the phenotype we observed, the expression of neutrophil markers were all included in down-regulated genes. Nonetheless, the expression of myeloid progenitor marker and macrophage marker  were not impaired in asxl1 mutants. We also found inflammatory cytokine and matrix metalloproteinases were upregulated after mutated asxl1. It suggests that neutrophil deficiency may stimulate the expression of some inflammatory cytokines and enhances the inflammatory responds. Therefore, transcriptome analysis mainly represented the disruption of neutrophil development.

overall_design: 3 days post fertilization (dpf) asxl1+/+ and asxl1-/- embryos from asxl1+/- intercross were collected and extract total RNA from the tails including CHT. Each sample is a pool of tails (about 20). Sequencing libraries were prepared from total RNA using Novogene NGS RNA Library Prep Kit. Sequencing was done on an Illumina NovaSeq sequencing platform to obtain 150bp 2 ´ 150 bp


title: Tissue microenvironment shapes distinct sets of machineries to regulate ILC2 properties [RNA-seq]

city: Shanghai

first: Ju

last: Qiu

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary: ILC2s from different tissues manifest distinct properties. To investigate the molecular mechanisms regulating tissue features of ILC2s, we performed single cell RNA-seq on purified ILC2s from 5 different tissues.

overall_design: ILC2s from the bone marrow, large intestine, lung, pancreas and small intestine from 6-week-old male wild-type mice were sorted by flow cytometry. ILC2s from bone marrow, large intestine, lung and pancreas were sorted as Lin(lineage)–ST2+CD25+ cells. And ILC2s from small intestine were sorted as Lin–Thy1intermediateCD45+KLRG1+ cells. Lineage markers were CD3, B220, CD11b, CD11c and FceRI. 30000 ILC2s from 5 tissues of 10 mice were subjected to scRNA-seq and two rounds of sequencing were performed on the each library of ILC2s from every tissue to obtain abundant reads and pooled for subsequent analysis.

first: Jinxin

first: Jingjing

last: Zhang

first: Lei

last: Shen

first: Yan

last: Ji


title: Activation of AhR by ITE in DCs induces differential gene expression over time.

summary: To evaluate the effects of AhR activation in dendritic cells (DCs) over time, DCs isolated from human blood or murine spleens were incubated with the AhR ligand ITE for 6 hours, 18 hours, or 72 hours. Treatment with ITE was found to induce transcriptional programs associated with immunoregulatory/ immunosuppressive mchanisms.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Dendritic cells isolated from peripheral blood of healthy human donors or from the spleens of healthy B6 mice were incubated with the AhR ligand ITE for 6 hours, 18 hours, or 72 hours.


title: Differential transcriptome profiling of P. aeruginosa PAO1 with oxythiamine treatment

status: Public on Aug 03 2021

city: Seongnam

first: Soojin

last: Jang

state: Gyeonggi

address: 16, Daewangpangyo-ro 712

department: Discovery Biology

country: South Korea

institute: Institut Pasteur Korea

summary: We report antibacterial potency of oxythiamine, which is a known transketolase inhibitor in eukaryotes. Oxythiamine inhibited the growth of P. aeruginosa PAO1 and clinical isolates in thiamine-depleted medium only. Metabolic and trascriptomic analyses indicated that oxythiamine was converted to oxythiamine pyrophosphate that subsequently inhibited several vitamin B1-dependent enzymes. Furthermore, a system-level perturbation of thiamine metabolism sensitized P. aeruginosa to multiple small-molecules informing the potential development of a rational drug combination.

overall_design: Transcriptomic observation of isolated RNA samples from P. aeruginosa PAO1 with or without oxythiamine treatment for 30 and 180 minutes

first: Hyung

last: Kim


title: Autophagy mutants show delayed chloroplast development during de-etiolation in carbon limiting conditions

city: Philadelphia

first: Diep

middle: R

last: Ganguly

state: PA

address: 433 S University Ave

department: Department of Biology

institute: University of Pennsylvania

summary: Autophagy is a conserved catabolic process that plays an essential role under nutrient starvation condition and influences different developmental processes. We observed that seedlings of autophagy mutants (atg2, atg5, atg7, and atg9) germinated in the dark showed delayed chloroplast development following illumination. The delayed chloroplast development was characterized by a decrease in photosynthetic and chlorophyll biosynthetic proteins, lower chlorophyll content, reduced chloroplast size, and increased levels of proteins involved in lipid biosynthesis. Confirming the biological impact of these differences, photosynthetic performance was impaired in autophagy mutants 12h post illumination. We observed that while gene expression for photosynthetic machinery during de-etiolation was largely unaffected in atg mutants, several genes involved in photosystem assembly were transcriptionally downregulated. We also investigated if the delayed chloroplast development could be explained by lower lipid import to the chloroplast or lower triglyceride (TAG) turnover. We observed that the limitations in the chloroplast lipid import imposed by trigalactosyldiacylglycerol1 are unlikely to explain the delay in chloroplast development. However, we found that lower TAG mobility in the triacylglycerol lipase mutant sugardependent1 significantly affected de-etiolation. Moreover, we showed that lower levels of carbon resources exacerbated the slow-greening phenotype whereas higher levels of carbon resources had an opposite effect. This work suggests a lack of autophagy machinery limits chloroplast development during de-etiolation, and this is exacerbated by limited lipid turnover (lipophagy) that physically or energetically restrains chloroplast development.

overall_design:
We used Arabidopsis (Arabidopsis thaliana) seeds of Col-0 as WT, four autophagic mutants atg2-1 (SALK_076727, Yoshimoto et al. 2009), atg5-1 (SAIL_129B07, Chen et al. 2015), atg7-2 (GABI_655B06, Lai et al. 2011) and atg9-2 (SALK_130796, Zhuang et al. 2017) which we referred as atg2, atg5, atg7 and atg9 respectively, a lipid thylakoid permease mutant tgd1 (Xu et al., 2003), a TAG lipase mutant (sugar-dependent 1-4) sdp1-4 (Eastmond, 2006; Fan et al., 2017) and the respective lipid and autophagy double mutants tgd1atg2-1, tgd1 atg5-1, sdp1atg2-1, and sdp1 atg5-1 (Fan et al., 2019).

Seeds were surface-sterilized and carefully dispensed on a stainless-steel wire mesh platform (mesh size 1 mm; 3 cm x 3 cm x 3 cm) layered previously with 1% sterilized agarose in a round plastic vessel containing 300 mL of liquid medium (1⁄4- strength Murashige and Skoog -MS- medium without vitamins, 1⁄4- strength Gamborg B5 vitamins solution, 2 mM MES, 1% [w/v] sucrose, pH 5.8). Seeds were grown for five days in the dark, then transferred to light (100-125 µE) at 22oC. Samples were collected in biological triplicate at 0, 12, and 24 post-illumination.

first: Akila

last: Wijerathna-Yapa

first: Barry

last: Pogson

first: A

last: Millar


title: Gene expression change after inactivation of IRF8

city: Cold Spring Harbor, Syosset

first: Chrsitopher

last: Vakoc

state: NEW YORK

address: 1 Bungtown Rd

institute: CSHL

summary: Cancer cell type-selective addiction of transcription-chromatin regulatory program   provides opportunities for therapeutic interventions. Here, we uncovered an IRF8-MEF2D transcription factor (TF) regulatory circuit as an acute myeloid leukemia (AML)-biased dependency. Combining CRISPR-based genetic screens, transcriptional analysis, and chromatin profiling, we demonstrated that a chromatin regulator, ZMYND8, directly regulates IRF8 and MYC expression through occupying AML-specific enhancer regions. ZMYND8 was essential for AML proliferation both in vitro and in vivo. The ZMYND8-occupied IRF8 enhancer was further characterized using Circular Chromosome Conformation Capture and CRISPRi-based perturbation assays and was observed in  primary patient cells. Importantly, mutagenesis experiments revealed that the PHD/Bromodomain/PWWP reader module is required for ZMYND8 tethering to leukemia-essential co-activator BRD4 for enhancer-mediated gene regulation. Our results rationalize ZMYND8 as a potential selective therapeutic target for modulating the IRF8/MYC transcriptional networks in AML.

overall_design: 2 sgRNAs targeting IRF8 at different sites and control sgRNA were tranducted into leukemia cell lines with lentivirus, 4 days after infection, cell samples were collected and RNA was extracted, followed by RNA-seq library preparation according standard protocol recommended by Illumina.

first: Bin

last: Lu


title: Effect of G0s2 and Rgs16 knockdown on hepatic transcriptome

first: Yilie

last: Liao

address: Kaiyuan Street No.190

institute: Bioland Laboratory

summary: We identified 2 leading gene candidates (G0s2 and Rgs16) in response to circadian, diet and genetic manipulations by a large-scale transcriptome analysis. To examine the impact of G0s2 and Rgs16 on liver functions, we carried out adenovirus-mediated liver-specific knockdown of both genes and performed RNA-seq analysis.

overall_design: Comparison between liver samples of shLacZ control and G0s2 or Rgs16 knockdown (shG0s2 or Rgs16) mice.

first: Xiaojie

last: Bai

first: Fangfang

last: Sun

first: Xia

last: Xiao


title: A Non-Canonical Raf Function Is Required for Dorsal-Ventral Patterning in Drosophila Embryogenesis

city: Singapore

first: Nicholas

last: Tolwinski

address: 16 #01-220, College Ave West

country: Singapore

institute: Yale-NUS College

summary: Embryonic development requires the establishment of directional axes.  In Drosophila, spatially discrete expression of transcription factors determines the anterior to posterior organization of the early embryo, while the Toll and TGF-beta signalling pathways determine the early dorsal to ventral pattern.  Embryonic MAPK/ERK signaling contributes to both anterior to posterior patterning in the terminal regions and to dorsal to ventral patterning during oogenesis and embryonic stages.  Here we describe a novel loss of function mutation in the Raf kinase gene, which leads to loss of ventral cell fates as seen through the loss of the ventral furrow, the absence of Dorsal/NF-kB nuclear localization, the absence of mesoderm determinants Twist and Snail, and the expansion of TGF-beta.  Gene expression analysis showed cells adopting ectodermal fates similar to loss of Toll signaling.  Our results combine novel mutants, live imaging, optogenetics and transcriptomics to establish a novel role for Raf, that appears to be independent of the MAPK cascade, in embryonic patterning.

overall_design: Embryo RNA profiles of  wild type (WT) and Raf926-/- Drosophila

middle: S

first: Prameet

last: Kaur

first: Nathan

last: Harmston

first: Ellora Hui Zhen

last: Chua


title: Characterization of Bregs-TLR/CpG by RNA-Seq

first: Qiang

last: Fu

state: Massachusetts

address: 55 Fruit St.

institute: Massachusetts General Hospital

summary: CpG-B cells and TLR-Bregs were obtained by giving isolated C57BL/6 splenic B cells either CpG ODN1668 stimulation for 3 days, or CpG stimulation with LPS, PMA, and ionomycin over the last 5 hours. RNA was extracted from all groups and analyzed using RNA-Sequencing and R.

overall_design: Total of 3 Naive B cell samples, 3 Bregs-CpG samples, and 2 Bregs-TLR samples

first: Kang

middle: M

last: Lee

first: Charles

middle: G

last: Rickert

first: Divyansh

last: Agarwal

first: James

last: Markmann


title: Single-cell RNA sequencing of peripheral blood reveals immune cell signatures in Alzheimer's disease

city: Beijing

first: Hui

last: Xu

address: Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Diseases

department: Department of neurology

institute: Xuanwu Hospital

summary: This study aimed to explore the molecular basis of peripheral immune cells and the   features of adaptive immune repertoire at a single cell level. We proﬁled 36,849   peripheral blood mononuclear cells from AD patients with amyloid-positive status and   normal controls with amyloid-negative status by 5' single-cell transcriptome and   immune repertoire sequencing using the cell ranger standard analysis procedure. We   revealed five immune cell subsets, CD4+ T cells, CD8+ T cells, B cells, natural killer   cells, and monocytes-macrophages cells, and disentangled the characteristic   alterations of cell subset proportion and gene expression patterns in AD. Thirty-one   cell type-specific key genes, comprising abundant human leukocyte antigen genes,   and multiple immune-related pathways were identified by protein-protein interaction   network and pathway enrichment analysis. We also found high-frequency   amplification clonotypes in T cells and B cells and decreased diversity in T cells in   AD. As clone amplification suggested the activation of an adaptive immune response   against specific antigens, we speculated that the peripheral adaptive immune response,   especially mediated by T cells, may have a role in the pathogenesis of AD. This   finding may also contribute to further research regarding disease mechanism and the   development of immune-related biomarkers or therapy.

overall_design:
Three patients with AD and two cognitively normal controls (NC)

>>>Submitter states: The analysis of TCR-seq and BCR-seq has not yet been performed<<<

first: Jian

last: Jia


title: Gene Changes in Hippocampus from Mice with Conditional Knockout of Hippocampal GR, MR, or both GR and MR

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Glucocorticoids are primary stress hormones that have been implicated in the pathogenesis of cognitive impairments and psychiatric illnesses.  The hippocampus expresses high levels of glucocorticoid (GR) and mineralocorticoid receptors (MR) which both bind glucocorticoids. However, the specific and cooperative roles played by GR and MR in mediating the direct actions of stress on the hippocampus are unknown. To elucidate the function of hippocampal GR and MR, we generated mice with conditional knockout of GR (GREmx1-cre), MR (MREmx1-cre), or both GR and MR (GRMREmx1-cre) in the hippocampus.  Genome-wide microarrays were performed on RNA isolated from the whole hippocampus to 1) identify genes subject to regulation by GR alone, MR alone, or both GR and MR and 2) identify the genes responsible for the morphological and behavioral phenotypes observed in these mice.

overall_design: Mice harboring a floxed GR allele (GRflox), MR allele (MRflox), or both GR and MR alleles (dflox) were crossed with Emx1-Cre mice to generate mice lacking GR (GREmx1-cre), MR (MREmx1-cre), or both GR and MR (GRMREmx1-cre) in the hippocampus, respectively.  Total RNA for microarray analysis was harvested from the whole hippocampus isolated from approximately 2.5-month old male dflox control mice and GREmx1-cre, MREmx1-cre, and GRMREmx1-cre knockout mice.

first: Shannon

middle: D

last: Whirledge

first: Robert

last: Oakley

first: John

middle: A

last: Cidlowski


title: RNA-seq of expanded human CRISPR/HDR-mediated FOXP3-KO naive Tregs, Cas9 naive Tregs, and conventional T cells

city: Vancouver

first: Megan

middle: K

last: Levings

address: 950 West 28th Ave

country: Canada

institute: University of British Columbia

summary: Treg cell therapy is a promising curative approach for a variety of immune-mediated conditions. CRISPR-based genome editing allows precise insertion of transgenes through homology-directed repair, but its use in human Tregs has been limited. We report an optimized protocol for CRISPR-mediated gene knock-in in human Tregs with high-yield expansion. To establish a benchmark of human Treg dysfunction, we target the master transcription factor FOXP3 in naive and memory Tregs. Although FOXP3-ablated Tregs upregulate cytokine expression, effects on suppressive capacity in vitro manifest slowly and primarily in memory Tregs. Moreover, FOXP3-ablated Tregs retain their characteristic protein, transcriptional, and DNA methylation profile. Instead, FOXP3 maintains DNA methylation at regions enriched for AP-1 binding sites. Thus, while FOXP3 is important for human Treg development, it has a limited role in maintaining mature Treg identity. Optimized gene knock-in with human Tregs will enable mechanistic studies and the development of tailored, next-generation Treg cell therapies.

overall_design: Flow-sorted human naive Tregs (CD4+CD25hiCD127loCD45RA+) were edited by CRISPR-mediated gene knock-in to achieve uniformly FOXP3-ablated cells and expanded for total 20 days. Flow-sorted conventional T cells (CD4+CD25loCD127hi) were expanded in parallel, without CRISPR editing. Briefly, cells were preactivated for 5 days, edited with CRISPR and homology-directed repair to ablate FOXP3 and knock-in sfGFP, and expanded for 7 days. Edited cells were sort-purified by sfGFP+, expanded for an additional 7 days, then rested overnight. RNA-seq was performed on samples across 4 independent donors.

first: A

last: Lam

first: M


title: Microarray analysis of hepatic gene expression from control,model,DSS group

city: Tianjin

first: Jiang

last: Miaomiao

address: Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, P. R. China

summary: Metabolic syndrome (MetS) is a pathological state of many abnormally metabolic sections. DSS is seldom reported about the application of MetS and the mechanism how DSS improves gut microbiadysbiosis and hepatic lipid homeostasis. Pharmacological actions were evaluated by comparison of transcriptomic assessments on liver tissues from fructose-fed rats. The aim of investigation was in order to find which pathways were altered by fructose and how DSS effected the metabolic pathways. Rats in control group were normally fed with food and water. Rats in model were fed with 15% fructose water and normal food. Rats in DSS group were intervened orally by Danggui-shaoyao-san extracts, besides the same fed way as model group. Total RNA was extracted from liver according to the test kit’s instruction. After a series of treatment, The cDNA was amplified and enriched by PCR and QC tested by Agilent 2100 Bioanalyzer&ABI StepOnePlus Real-Time PCR System (Agilent Technologies Inc, California). Finally the data was sequenced by Illumina platform and the reads were compared by HISAT2 software. Differential analysis was performed by DEGseq&DESeq platform. Finally, all the evidences showed that fructose could induce the differential gene changes and metabolite discordances and DSS could regulate back these abnormalities especially in carbohydrate, lipid and amino acids at the Level 2 of KEGG pathway.

overall_design: Examination of hepatic gene expression from 3 different groups in rats. 3 samples in each group. Are there control,model,DSS group.

first: Miaomiao

last: Jiang

first: Jing

last: Yin

first: Shengjie

last: Huang


title: Genome-wide ChIPseq analysis of COUP-TFII, and HNF4α following 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)-treatment in mouse liver

city: East Lansing

first: Timothy

last: Zacharewski

state: MI

address: 603 Wilson Rd., BCH Building RM#212

department: Biochemistry and Molecular Biology

institute: Michigan State University

summary: Treatment of mice with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) has been shown to disrupt many physiological processes including hepatic lipid metabolism, bile acid homeostasis, glucose metabolism, iron and heme homeostasis, and one-carbon metabolism. TCDD disrupts these metabolic pathways mediated by the aryl hydrocarbon receptor (AhR). We have previously shown that the AhR localizes to genomic regions possessing DNA motifs that also contain binding sites for other transcription factors, implicating potential co-operation between the AhR and these other transcription factors in the regulation of target genes. Two possible co-operating transcription factors include HNF4α and COUP-TFII. To investigate interactions between AhR, HNF4α and COUP-TFII hepatic ChIP-seq analysis was performed for HNF4α and COUP-TFII mice treated with TCDD for 2 hours, to supplement pre-existing AhR ChIP-seq data. ChIP-seq analysis revealed genome-wide changes in COUP-TFII and HNF4α binding following treatment with TCDD, with 11,688 and 9,547 genomic regions possessing differential enrichment, respectively. These differentially enriched regions for COUP-TFII and HNF4α fell within the intragenic region of 6,846 and 5,762 genes, respectively. When supplemented with pre-existing AhR ChIP-seq data, AhR, HNF4α and COUP-TFII were found to co-bind to the intragenic region of 6,376 genes.

overall_design: Five biological replicates, pooled

first: Giovan

last: Cholico

first: Rance

last: Nault


title: Tissue microenvironment shapes distinct sets of machineries to regulate ILC2 properties [ATAC-seq]

first: Ju

last: Qiu

summary: ILC2s from different tissues manifest distinct properties. To investigate the molecular mechanisms regulating tissue features of ILC2s, we performed ATAC-seq on purified ILC2s from 5 different tissues.

overall_design: ILC2s from the bone marrow, large intestine, lung, pancreas and small intestine from 6-week-old male wild-type mice were sorted by flow cytometry. ILC2s from bone marrow were sorted as Lin(lineage)–ST2+CD25+ cells. ILC2s for large intestine, lung and pancreas were sorted as Lin–CD45+CD127+ST2+CD25+. And ILC2s from small intestine were sorted as Lin–CD127+Thy1intermediateCD45+KLRG1+ cells. Lineage markers were CD3, B220, CD11b, CD11c and FceRI. Biological duplicates of 50000 ILC2s from 5 tissues of 10-16 mice were subjected to ATAC-seq sequencing analysis.

first: Jinxin

first: Jingjing

last: Zhang

first: Lei

last: Shen

first: Yan

last: Ji


title: Mechanism of exosomes involved in osteoimmunity promoting osseointegration around titanium implants with micro-/nano-texture hierarchical topography

city: Jinan

first: Huiqiang

last: Sun

state: Shandong

address: #44-1 wenhuaxilu Road

department: Prosthodontics

institute: Shandong school and hospital of stomatology

type: Non-coding RNA profiling by high throughput sequencing

summary: Exosomes are nanoscale extracellular vesicles. Several studies have shown that exosomes participate in intercellular communication and play a key role in osseointegration. However, it is unclear whether exosomes and their contents participate in the communication between the immune and skeletal systems in the process of osseointegration. In this study, we obtained smooth titanium disks by polishing and micro-/nano-texture hierarchical topography titanium disks by sandblasted large-grit acid-etched (SLA) technology combined with alkali thermal reaction. After stimulating rat RAW264.7 cells with these two kinds of titanium disks, we co-cultured the MC3T3-E1 cells and the RAW264.7 cells, obtained and identified the exosomes derived from RAW264.7 cells, and studied the effect of the osteoimmune microenvironment and the exosomes on the osseointegration of rat MC3T3-E1 cells. Cell counting kit-8 (CCK-8), real time quantitative PCR, western blotting, alizarin red staining, and quantitative and confocal fluorescence microscopy were used to study the effects of exosomes on MC3T3-E1 cells; RNA sequencing and correlation analysis were performed. We found that the osteoimmune microenvironment could promote the osseointegration of MC3T3-E1 cells. We successfully isolated exosomes and found that RAW264.7 cell-derived exosomes can promote osteogenic differentiation and mineralization of MC3T3-E1 cells. Through RNA sequencing and gene analysis, we found differentially expressed microRNAs that targeted the signal pathways that may be related, such as mTOR, AMPK, Wnt, etc, and thus provide a reference for the mechanism of osteoimmunue regulation of implant osseointegration. The study further elucidated the mechanism of implant osseointegration and provided new insights into the effect of exosomes on implant osseointegration, and provided reference for clinical improvement of implant osseointegration and implant success rate.

overall_design: control sample and experiement sample

first: Ting

first: Mengyang

first: Xiaojie

first: Peng

last: Yao


title: Utilization of transcriptome, small RNA, and degradome sequencing to provide insights into drought stress and re-watering treatment in Medicago ruthenica (Degradome-Seq)

city: Hohhot

first: Rui

last: Shi

address: No.306, Zhaowuda Road, Saihan District, Hohhot

institute: Inner Mongolia Agricultural University

summary: Drought is a major limiting factor in foraging grass yield and quality. Medicago ruthenica is a high-quality forage legume with drought resistance, cold tolerance, and strong adaptability. In this study, we integrated transcriptome, small RNA, and degradome sequencing in identifying drought response genes, miRNAs, and key miRNA-target pairs in M. ruthenica under drought and re-watering treatment conditions. A total of 3,905 genes and 50 miRNAs (45 conserved and 5 novel miRNAs) were significantly differentially expressed between the re-watering (RW) vs. drought (DS) comparison and control (CK) groups. The degradome sequencing analysis revealed that 348 miRNAs (37 novel and 311 conserved miRNAs) were identified with 6,912 target transcripts, forming 11,390 miRNA-target pairs in the three libraries. There were 38 differentially expressed targets from 16 miRNAs in DS vs. CK, 31 from 11 miRNAs in DS vs. RW, and 6 from 3 miRNAs in RW vs. CK; 21,18, and 3 miRNA-target gene pairs showed reverse expression patterns in DS vs. CK, DS vs. RW, and RW vs. CK comparison groups, respectively. These findings provide valuable information for further functional characterization of genes and miRNAs in response to abiotic stress, in general, and drought stress in M. ruthenica, and potentially contribute to drought resistance breeding of forage in the future.

overall_design: Leaves degradome profiles of Medicago ruthenica were constructed by sequencing from three leaf samples (CK: control, DS: plants under drought stress, RW: plants re-watering after drought stress), each with three biological replicates.

first: Fugui

last: Mi


title: Tissue microenvironment shapes distinct sets of machineries to regulate ILC2 properties

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Gene expression of two Ewing sarcoma cell lines (A-673, ES7), treated with triapine (3-AP) or vehicle (DMSO)

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

institute: German Cancer Research Center (DKFZ)

summary: This dataset comprises transcriptome data of two Ewing sarcoma cell lines (A-673, ES7) after treatment with triapine (3-AP) or vehicle (DMSO) for 72h.

overall_design: 8 samples were normalized (log2) with Affymetrix Expression Console Software (v1.4) using SST-RMA algorithm. Gene expression data were annotated at gene level with the Affymetrix library for Clariom D arrays (human).

first: Shunya

last: Ohmura

last: Grünewald


title: Transcriptome analysis of total RNA from Rhodobacter sphaeroides 2.4.1 wildtype and StsR (RSs0827) deletion strain during different growth phases

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

institute: Justus-Liebig University Gießen

summary: The sRNA StsR (formerly RSs0827) was first described as an sRNA induced upon iron starvation and was later demonstrated to be the most highly induced RNA in late stationary phase in the phototrophic Alphaproteobacterium R. sphaeroides. StsR is under control of RpoHI/RpoHII and therefore induced by multiple stress factors. To investigate the function of this sRNA on the hole transcriptome of R. sphaeroides we performed RNAseq with cultures of the exponential growth (6 h) phase, stationary growth phase (72 h / 144 h) and outgrowth phase. Cultures were grown under microaerobic growth conditions in biological triplicates.

overall_design: This data includes the transcriptome data of two different strains each in triplicates: Rhodobacter sphaeroides 2.4.1 (wildtype) and R. sphaeroides 2.4.1 StsR deletion strain (d0827). Total RNA of all strains was isolated and sequenced.

first: Katrin

last: Eisenhardt

first: Konrad

last: Förstner


title: Rotavirus susceptibility of antibiotic-treated mice ascribed to diminished expression of IL-22

city: London

first: Andreas

last: Wack

address: 1 Midland Road

institute: The Francis Crick Institute

summary:
We wanted to identify effector molecules which confer rotavirus resistance in microbiota-depleted mice
We used microarrays to analyze the global programme of gene expression in response to IL22 treatment in the ileum of antibiotic-treated Ifnlr1-/- mice

overall_design: Saline control or IL-22 treated animals were sacrified 4 hours post treatment and RNA extracted from ileum; rep 1 through rep 5 represent independent biological replicates of the same mouse treatment.

first: Daniel

last: Schnepf

first: Peter

last: Staeheli

first: Stefania

last: Crotta


title: Genome-wide DNA methylation profile of expanded human CRISPR/HDR-mediated FOXP3-KO naive Tregs, Cas9 naive Tregs, and conventional T cells

first: Megan

last: Levings

overall_design: Flow-sorted human naive Tregs (CD4+CD25hiCD127loCD45RA+) were edited by CRISPR-mediated gene knock-in to achieve uniformly FOXP3-ablated cells and expanded for total 20 days. Flow-sorted conventional T cells (CD4+CD25loCD127hi) were expanded in parallel, without CRISPR editing. Briefly, cells were preactivated for 5 days, edited with CRISPR and homology-directed repair to ablate FOXP3 and knock-in sfGFP, and expanded for 7 days. Edited cells were sort-purified by sfGFP+, expanded for an additional 7 days, then rested overnight. Genome-wide DNA methylation was assessed by Illumina MethylationEPIC from samples across 5 independent donors.

first: A

last: Lam

first: D

middle: T

last: Lin

first: M


title: RNA-sequencing identifies global transcriptional changes in peripheral CD4+ cells during active esophagitis and following epicutaneous immunotherapy in eosinophilic esophagitis.

city: Philadelphia PA

first: Melanie

middle: A.

last: Ruffner

address: 3615 Civic Center Blvd, Abramson Research Center

department: Allergy & Immunology

institute: Children's Hospital of Philadelphia

summary: Immunotherapy strategies have been studied for IgE-mediated food allergies but have not been studied for non-IgE mediated food allergy disorders, including eosinophilic esophagitis.  We interrogated the transcriptional signatures of peripheral CD4+ cells isolated from pediatric eosinophilic esophagitis patients enrolled in a phase IIa clinical trial of milk-antigen epicutaneous immunotherapy. We analyzed differential expression in peripheral CD4+ cells before therapy in patients before and after milk-exclusion diet. RNA-sequencing analysis revealed that there were 244 differentially expressed genes in peripheral blood CD4+ cells of EoE patients consuming milk versus those eliminating it, and 129 DEGs in CD4+ cells isolated after EPIT versus after placebo (FDR<0.05). Gene set enrichment analysis identifies enrichment of hallmark interferon-a and -g response signatures in peripheral CD4+ T cells from EoE patients during active disease on a milk-containing diet. In post-EPIT therapy samples, our analysis identifies enrichment in T-cell receptor signaling, antigen presentation, costimulation, and cytokine signaling pathways. These data suggest a unique peripheral CD4+ T cell gene signature is present in EoE patients during active disease. We observe a distinct transcriptional profile post-EPIT therapy in EoE patients, suggesting that EPIT alters CD4+ responses in EoE patients.

overall_design: Peripheral blood samples were collected from 15 of 20 patients enrolled in in a clinical trial of milk antigen epicutaneous immunotherapy (EPIT) for EoE (PMID: 31100455). Samples were collected from three timepoints. (1) before therapy, on milk-containing diet (2) before therapy, on milk-avoidance diet (3) after EPIT or placebo therapy.  CD4+ T cells were isolated from the peripheral blood samples using magnetic bead positive isolation. Total RNA was isolated and sequenced from isolated CD4+ cell population.

first: Zhe

last: Zhang


title: Utilization of transcriptome, small RNA, and degradome sequencing to provide insights into drought stress and re-watering treatment in Medicago ruthenica (RNA-seq)

first: Rui

last: Shi

overall_design: Leaves mRNA profiles of Medicago ruthenica were constructed by deep sequencing from three leaf samples (CK: control, DS: plants under drought stress, RW: plants re-watering after drought stress), each with three biological replicates.


title: Utilization of transcriptome, small RNA, and degradome sequencing to provide insights into drought stress and re-watering treatment in Medicago ruthenica (miRNA-seq)

overall_design: Leaves miRNA profiles of Medicago ruthenica were constructed by sequencing from three leaf samples (CK: control, DS: plants under drought stress, RW: plants re-watering after drought stress), each with three biological replicates.

first: Fugui

last: Mi


title: Comparison of genome-wide DNA methylation profiles of human fetal tissues conceived by in vitro fertilization and natural conception

first: Ye

last: Liu

state: Shanghai

address: No. 1961, Huashan Road

institute: The International Peace Maternity and Child Health Hospital

summary: Genome wide DNA methylation profiling of fetal tissue from elective terminations of pregnancy and multifetal pregnancy reduction. The Illumina Infinium HumanMethylation 450k BeadChip array was used to obtain DNA methylation profiles across approximately 453,093 CpGs in fetal tissue samples.

overall_design:
Bisulphite converted DNA from the 24 samples were hybridised to the Illumina Infinium HumanMethylation 450k BeadChip array.

Please note that the ETP sample group (indicated in the sample characteristics field; SAMPLE 1 to 12) is from natural pregnancy, and the MFPR group (SAMPLE 13 - 24) are from IVF.

first: Xin-Zhu

last: Li


title: Transcriptome analysis for modulating ubiquitin siganlling in the amniote embryo via phosphoregulation of the E2 enzyme UBE2D3

first: Yi-Fang

last: Wang

address: Du Cane Road

institute: MRC LMS

summary:
Purpose: Understanding the transcriptional effects of a gain of function mutation of the E2 enzyme UBE2D3 in embryonic stem cells
Methods: mRNA profiles of wt E14 ES cells and UBE2D3 Ser138Ala mutant ES cells were generated

overall_design: 6 samples examined: 3 WT E14 ES cells and 3 S138A mutant E14 ES cells

first: Monica

last: Roman-Trufero

first: Niall

last: Dillon


title: Transcriptome sequencing of A.thaliana leaves after exposure to silver nanoparticles.

city: haikou

first: zhang

last: chuanling

address: renmin Road NO.58

institute: Hainan University

summary: RNA-Seq analysis was used for deep sequencing of transcriptome to detected molecular mechanisms of silver nanoparticles (AgNPs) and distinguish the effects of Arabidopsis thaliana exposure to AgNPs and Ag+.We identified 626 and 767 differentially expressed genes (DEGs) influenced by AgNPs and Ag+ respectively.302 genes were specifically regulated by the AgNPs treatment indicates that the  nanoparticle-specific effects.This study provide a valuable resource for the discovery of genes related to special toxicity mechanism of AgNPs.

overall_design: Transcriptome of nine A.thaliana leaves were generated by deep sequencing using Illumina.

first: Chuan

middle: L

first: Hong

last: Jiang


title: The next-generation sequencing was helpful for the quantitative analysis of the normal control group and the liver fibrosis group

city: changsha

first: Wu

last: Cichun

address: Xiangya Road Street, Kaifu District

institute: Cichunwu

summary: Ten snap-frozen liver tissues were used for RNA sequencing (RNA-seq) and were obtained from 8 patients who underwent surgical resection for the treatment of HBV-associated liver cancer in the liver fibrosis group (n=4) or hemangioma in the control group (n=4). RNA-seq showed that 1246 genes were aberrantly expressed with more than log2-fold change in liver fibrosis tissues than in normal control tissues (P<0.05). Among these, 687 genes were significantly up-regulated and 559 genes were down-regulated.

overall_design: Normal liver tissue and liver fibrosis patients.

first: Xin

last: Ni

first: Shifang

last: Peng

first: Lei

last: Fu

first: Cichun

last: Wu


title: Utilization of transcriptome, small RNA, and degradome sequencing to provide insights into drought stress and re-watering treatment in Medicago ruthenica


title: Single-cell transcriptomics of normal pancreas, intraductal papillary mucinous neoplasm, and pancreatic adenosquamous carcinoma reveals the heterogeneous progression of pancreatic ductal and stromal cells

first: Han

address: Gongti Road

department: HBP

institute: Beijing Chaoyang hosipital

summary:
Background: Single-cell RNA sequencing (scRNA-seq) contributes to discovering intrinsic heterogeneity of pancreatic adenosquamous carcinoma (PASC), a lethal human malignancy. However, the gene-pattern variations within ductal and stromal cells remain unclear.
Methods: We fulfilled scRNA-seq profiling with one healthy donor pancreas, one intraductal papillary mucinous neoplasm (IPMN), and one PASC sample tissue. Multiple bioinformatics analyses were used to investigate the transcriptomics abnormalities from normal stage to tumor formation.
Results: We identified ten subpopulations from 10,346 single cells, including myeloid, immune, ductal, fibroblast, acinar, stellate, endothelial, and malignant cells. Within our analysis, pancreatic cancer cells were further divided into five clusters; notably, cluster 1 exhibited stem-like phenotypes, such as UBE2C, ASPM, and TOP2A. We also found that S100A2 could be a specific biomarker for tumor cells, relating to PASC progression. LGALS1, NPM1, RACK1, and PERP were upregulated gradually from ductal to malignant cells. Furthermore, the level of copy number variation in ductal and cancer cells was significantly greater than reference cells. The expression of EREG, FCGR2A, FCGR2A, and CCL4L2 increased in myeloid cells along with tumor development, while cancer-associated fibroblast could induce the immunosuppressive tumor microenvironment, promoting pancreatic cancerogenesis. Finally, we demonstrated that EGFR-associated ligand-receptor pairs were activated in stromal to malignant cell communication.
Conclusion: This study revealed the variations of ductal and stromal cells, defined cancer-associated signaling pathways, and deciphered cellular interactions following PASC progression. Thus, we provided valuable information to further understand the crucial regulatory mechanisms that embrace the potential therapeutic targets for PASC.

overall_design: mRNA profiles of normal pancreas, intraductal papillary mucinous neoplasm, and pancreatic adenosquamous carcinoma

last: Zhao


title: Characterization of the blood-brain barrier in genetically diverse laboratory mouse strains

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

summary: Genetic variation in the population has an influence on the manifestation of monogenic as well as multifactorial disorders, with the underlying genetic contribution dependent on several interacting variants. Common laboratory mouse strains used for modelling human disease lack the genetic variability of the human population. Therefore, outcomes of rodent studies show limited correlation with human disease. The functionality of brain vasculature is an important modifier of brain diseases. Importantly, the restrictive interface between blood and brain – the blood-brain barrier (BBB) serves as a major obstacle for CNS drug delivery. Using genetically diverse mouse strains, we aimed to investigate the phenotypic and transcriptomic variation of the intact BBB in different inbred mouse strains.We investigated the heterogeneity of brain vasculature in recently wild-derived mouse strains (CAST/EiJ, WSB/EiJ, PWK/PhJ) and long-inbred mouse strains (129S1/SvImJ, A/J, C57BL/6J, DBA/2J, NOD/ShiLtJ) using different phenotypic arms. We used immunohistochemistry and confocal laser microscopy followed by quantitative image analysis to determine vascular density and pericyte coverage in two brain regions – cortex and hippocampus. Using a low molecular weight fluorescence tracer, sodium fluorescein and spectrophotometry analysis, we assessed BBB permeability in young and aged mice of selected strains. For further phenotypic characterization of endothelial cells in inbred mouse strains, we performed bulk RNA sequencing of sorted endothelial cells isolated from cortex and hippocampus. We did not detect differences in cortical and hippocampal vessel density and pericyte coverage among all the investigated strains. The staining patterns of endothelial arteriovenous zonation markers were similar in different strains. BBB permeability to a small fluorescent tracer, sodium fluorescein, was also similar in different strains. Transcriptomic analysis of endothelial cells revealed that sex of the animal was a major determinant of gene expression differences. In addition, the expression level of several genes implicated in endothelial function and BBB biology differed between wild-derived and long-inbred mouse strains. Our analysis shows that although there were no major differences in parenchymal vascular morphology and BBB permeability between investigated mouse strains or sexes, transcriptomic differences of brain endothelial cells point to variation in gene expression of the intact BBB. These baseline variances might be confounding factors in pathological conditions that may lead to a differential functional outcome dependent on the sex or genetic polymorphism.

overall_design: We investigated the heterogeneity of brain vasculature in recently wild-derived mouse strains (CAST/EiJ, WSB/EiJ, PWK/PhJ) and long-inbred mouse strains (129S1/SvImJ, A/J, C57BL/6J, DBA/2J, NOD/ShiLtJ) using RNA sequencing of brain endothelial cells.

first: Johanna

last: Schaffenrath

first: Sheng-Fu

last: Huang

first: Mauro

last: Delorenzi

first: Annika

last: Keller


title: IL-12 regulates type 3 immunity through interfollicular keratinocytes in psoriasiform inflammation

city: Zürich

first: Pascale

last: Zwicky

address: Wintherturerstrasse 190

institute: University of Zurich

summary: Psoriasis is a chronic inflammatory skin disorder underpinned by dysregulated cytokine signaling. Drugs neutralizing the common p40 subunit of IL-12 and IL-23 represented a therapeutic breakthrough; however, new drugs that block the IL-23p19 subunit and spare IL-12 are more effective, suggesting a regulatory function of IL-12. In order to pinpoint the cell type and underlying mechanism of IL-12 mediated immune-regulation in psoriasis we generated a conditional Il12rb2-knockout (KO)/reporter mouse strain. We detected Il12rb2 expression in T cells and a specific subset of interfollicular (IF) keratinocytes. Analysis of scRNAseq data from psoriasis patients confirmed this expression pattern in the human skin. Mechanistically, deletion of Il12rb2 in the keratinocyte compartment led to exacerbated psoriasiform inflammation. Protective IL-12 signaling blocked the hyperproliferation of keratinocytes, maintained skin barrier integrity, and, importantly, diminished disease-driving IL-23/type 3 immune circuits. Collectively, we provide a potential explanation for the superior efficacy of IL-23p19 inhibitors in psoriasis and describe an unperceived role of IL-12 in maintaining skin epithelial cell homeostasis.

overall_design: Gene expression analysis using total RNA from murine skin interfollicular keratinocytes. K14Cre/+ Il12rb2fl/fl and Il12rb2fl/fl mice were topically treated with Aldara cream (5% Imiquimod)  for 1 day or left untreated. Interfollicular keratinocytes were FACS sorted.

first: Florian

last: Ingelfinger

first: Bruno

last: Silva de Melo

first: Fiorella

last: Ruchti

first: Stefanie

last: Schärli

first: Nicole

last: Puertas

first: Mirjam

last: Lutz

first: Truong

last: Phan

first: Thomas

last: Kündig

first: Mitchell

middle: P

last: Levesque

first: Julia-Tatjana

last: Maul

first: Christoph

last: Schlapbach

first: Salomé

last: LeibundGut-Landmann

first: Sarah

last: Mundt

first: Burkhard

last: Becher


title: Gene expression profile of U2-OS control and NSD3 knockdown cells

city: Toronto

first: Jinchang

last: Lu

state: Ontario

address: 101 College Street

institute: Princess Margaret Cancer Centre, University of Toronto

summary: Osteosarcomas (OS) have highly chaotic genomes, yet their cancer drivers are poorly defined. Leveraging cross-species OS genomics we identify the frequent amplification of NSD3, a histone lysine methyltransferase and expose the NSD3-ARID3A axis as a core pathway in osteosarcomagenesis. Loss- and gain-of-function studies with CRISPR-Cas9 and lentivirus systems establish the causal role of NSD3 in OS tumor growth and spontaneous metastasis.

overall_design: Expression microarrays are performed to study the mechanism of NSD3 on promoting OS progression

first: Yang

last: Shao

first: Geoffery

last: Wood

first: Rama

last: Khokha


title: Canine pimary osteosarcoma tissues vs. matched lung metastases

type: Genome variation profiling by genome tiling array

summary: Osteosarcomas (OS) have highly chaotic genomes, yet their cancer drivers are poorly defined. Given that cancer genes are conserved among mammals, cross-species genomics of naturally arising cancers opens a powerful approach to identifying oncogenic drivers to broaden the therapeutic opportunities for aggressive cancers. Here, we utilized a dog-to-human cross-species genomics combined with gain- and loss-of-function analysis to uncover novel OS driver genes.

overall_design: Eight primary tumor samples compared with matched lung metastases

middle: W

first: Geoffrey


title: Histone H2A.X Phosphorylation Activates Caspase-Induced Chromatin Condensation in Late Stage Erythropoiesis

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

summary: Condensation of chromatin prior to enucleation is an essential component of terminal erythroid maturation, and defects in this process are associated with inefficient erythropoiesis and anemia. However, the mechanisms involved in this phenomenon are not well understood. Here, we identify a novel role for the histone variant H2A.X in erythropoiesis. We find in multiple model systems that this histone is essential for normal maturation and the loss of H2A.X in erythroid cells results in dysregulation in expression of erythroid specific genes as well a nuclear condensation defect. In Addition, we demonstrate that erythroid maturation is characterized by phosphorylation at both S139 and Y142 during late stage erythropoiesis. Knockout of the kinase BAZ1B/WSTF results in loss of Y142 phosphorylation and similar to loss of H2A.X, a defect in nuclear condensation. In this study, we present a model in which post-translational modifications on histone H2A.X during terminal erythroid maturation leads to Caspase-Induced Chromatin Condensation (CICC). In this novel pathway, although apoptosis is specifically suppressed, aspects of the apoptotic pathway remain active to drive terminal erythroid maturation. Suggesting that terminal erythroid maturation is indeed is a unique form of apoptosis.

overall_design: RNA-Seq of H2A.X and BAZ1B WT and KO HUDEP-2 cells at D0 and D6 of differentiation.

first: Nazish

last: Jeffery

first: Michael

last: Bulger


title: Gene expression signatures for human non-diabetic (hND) islets and human type 2 diabetes mellitus (hT2DM) islets

first: shusen

last: wang

address: No.24, Fukang Road

department: Organ Transplant Center

institute: Tianjin First Central Hospital

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: We employed a microarray as a discovery platform to identify the differential gene expressions between hND islets and hT2DM islets. 4805 genes with differential expression (fold change >2) were manifested in hT2DM islets. Inflammatory response and immune response were the mostly upregulated biological processes distinguished betwee hND islets and T2DM islets. Results provided insight into the molecular mechanisms in T2DM.

overall_design: Gene expression in human islets was measured after islets were isolated and purified. Human islet samples (>90% purity) were collected from two hND organ donors (sample H046, HE002) and two hT2DM organ donors (sample HE003_Islets, HE005_Islets).

first: Shusen

last: Wang


title: Effect of ORY-2001, ORY-LSD1, FTY720 on gene expression in EAE mice.

city: Cornella de Llobregat

first: Tamara

last: Maes

state: Barcelona

address: Carrer Sant Ferran 74

department: R&D

institute: Oryzon Genomics S.A.

summary: Gene expression analysis in the spinal cord and brain of vehicle-treated and ORY-2001 and ORY-LSD1 treated EAE mice in the subchronic (SC) and of ORY-2001 and ORY-LSD1 in the effector (E) phase in EAE mice

overall_design: Compiled data of 2 two-colour experiments, each experiment performed on spinal cord and brain of vehicle-treated and compound treated EAE mice. Three replicates per array for each gene probe.


title: Gene expression of two Ewing sarcoma cell lines (A-673, ES7), transduced with inducible shControl or two different shRNA against RRM2

first: Thomas

last: Grunewald

summary: This dataset comprises transcriptome data of two Ewing sarcoma cell lines (A-673 and ES7) after knockdown of the gene RRM2

overall_design: 12 samples were normalized (log2) with Affymetrix Expression Console Software (v1.4) using SST-RMA algorithm. Gene expression data were annotated at gene level with the Affymetrix library for Clariom D arrays (human).

first: Shunya

last: Ohmura

last: Grünewald


title: GATM PPMO knockdown affects host response to H1N1 influenza infection in mouse lungs

status: Public on Aug 02 2021

city: La Jolla

first: Max

last: Chang

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

summary: The GATM gene shows strong transcriptional regulation during influenza infection and increased GATM transcription correlates with peak viral titers in the lung. In order to investigate an in vivo role for GATM during influenza infection, we created a peptide-conjugated phosphorodiamidate morpholino oligomer (PPMO) to disrupt GATM translation. In our study, mice received a GATM-specific PPMO or scrambled PPMO once per day for two days, and then were subsequently infected with an H1N1 (A/California/04/2009) strain of IAV or PBS as a mock infection control. Mouse lungs were harvested three days post-infection and analyzed via RNA sequencing.

overall_design: Two-factor transcriptome comparison of mice treated with GATM PPMO or control (scramble) PPMO and either infected with H1N1 influenza or mock-infected with PBS. For each condition, samples were generated in either triplicate or quadruplicate.

first: Leah

last: Shriver

first: Carles

last: Martinez-Romero


title: Protective heterologous T cell immunity in COVID-19 induced by MMR and Tdap vaccine antigens

city: Davis

first: Monica

last: Britton

address: 451 Health Sciences Dr., Rm. 1300

department: Genome Center Service Cores

institute: University of California, Davis

summary: High correlation was observed between T cell responses to SARS-CoV-2 and MMR and Tdap vaccine proteins in infected and uninfected individuals; the overlapping T cell population contained an effector memory T cell subset previously implicated in protective anti-viral immunity and their activation required APC-derived IL-15, known to sensitize T cells to activation. We were able to detect cross-reactive TCR repertoire  in antigen experienced T cells recognizing SARS-CoV-2, MMR and Tdap epitopes using clonotyping and scRNA-seq. Indices of disease severity were reduced in MMR or Tdap vaccinated individuals by 32-38% and 20-23% respectively, among 73.582 COVID-19 positive patients.

overall_design:
Total of 12 human samples, T cell samples from 3 controls and 3 patients were analyzed for the study. 3 Control and 3 patient samples were treated with SARS-CoV-2 antigens and 3 samples from patients were treated with MMR and 3 samples were treated with Tdap antigens.

Submitter states "The sequencing was performed by an outside company; we are attempting to locate the fastq files"

first: Matthew

last: Settles

first: Vijayashree

last: Mysore


title: Transcriptome profile of MafB-cKO of podocyte

city: Tsukuba

first: Toshiaki

last: Usui

state: Ibaraki

address: 1-1-1 Tennoudai

department: Nephrology

institute: University of Tsukuba

summary: The transcription factor MafB is essential for differentiation and foot process formation of podocytes. In order to identify the downstream targets of MafB, we analyzed the Mafb-deficient podocyte by RNA-seq. We found slit diaphragm-related protein (Nphs1, Magi2), Rho GTPase-activating protein (Arhgap24, Iqgap2) and podocyte-specific transcription factor (Tcf21) were significantly reduced in MafB cKO glomeruli. This indicates that one of these factors might be directly regulated by MafB to maintain its function in podocyte maintenance.

overall_design: Examination of 6 samples (3 Control and 3 Mafb-cKO podocyte ). Each sample contains RNA  from 1 mouse. Paired-end RNA sequencing was performed with NextSeq500 sequencer (Illumina).

first: Usui

last: Toshiaki

first: Hossam

last: Shawki

first: Naoki

last: Morito

first: Masafumi

last: Muratani

first: Michito

last: Hamada

first: Satoru

last: Takahashi


title: CD93+ and CD93- HSCs comparison [ATAC-Seq]

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Hematopoietic stem cells (HSCs) are characterized by their ability to generate all blood cells while retaining their self-renewal capacity. While it is convenient to believe that HSCs represent a homogenous population, several evidences do not support this notion.  Here we identified and characterized a HSC population that expressed CD93 on their membrane. This population showed strong molecular dHSC signature, combined with activation features. Thereby, suggesting that they represent an intermediate state between quiescent and active HSCs being more prone to respond upon alterations in the hematopoietic lineage

overall_design: ATAC-seq from sorted HSC (LSK+CD34-CD48-Flt3-Slam1+) CD93+ or CD93-

first: Cecilia

last: Rodrigues


title: CD93+ and CD93- HSCs comparison

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Comprehensive molecular profiling of UV-induced metastatic melanoma in Nme1/Nme2-deficient mice reveals novel genes associated with progression and survival in human patients

city: Los Angeles

first: Zarko

last: Manojlovic

state: California

address: 1450 Biggy St

institute: University of Southern California

summary:
Purpose: Herein we demonstrate that UV-induced melanomas of low metastatic potential in mice that overexpress HGF and harbor deletion of the Ink4a/p16 locus (HP strain) are converted to highly metastatic forms by virtue of hemizygous deletion of the metastasis suppressor genes Nme1 and Nme2 (HPN strain). The striking difference in metastatic activity between HP and HPN melanomas strains provided a powerful system for identifying molecular profiles associated with metastatic activity.
Methods: Primary and metastatic melanoma RNAseq profiling.
Results: RNA-seq analysis of primary melanomas identified a 32-gene expression signature that was strongly associated with the HPN genotype and lung metastatic activity (HPN lung metastasis signature, or HPN-LMS). Expression of the HPN-LMS was highly predictive of overall survival in human cohorts of cutaneous melanoma (SKCM) and uveal melanoma (UVM) patients of The Cancer Genome Atlas (TCGA).
Conclusions: Three HPN-LMS genes (ARRDC3, NYNRIN, RND3) associated with longer survival in SKCM and/or UVM patients exhibited strong anti-invasion activity in human melanoma cells, consistent with roles as effectors of the metastasis suppressor functions of Nme1 and Nme2. The HP/HPN mouse paradigm has thus yielded a network of potential therapeutic targets and prognostic markers for clinical management of metastatic melanoma.

overall_design: RNAseq of primary and metastatic melanomas in Nme1+/- / Nme2+/- mouse strain.

first: David

last: Kaetzel

first: John

last: Carpten


title: CD93+ and CD93- HSCs comparison [RNA-Seq]

overall_design: Bulk RNA seq from sorted HSC (LSK+CD34-CD48-Flt3-Slam1+) CD93+ or CD93-


title: Transcriptome changes in forebrain neuron-specific farneyltransferase knockout in APP/PS1 mice

city: Minneapolis

first: Ling

last: Li

state: MN

address: 2001 6th Street SE

department: Experimental and Clinical Pharmacology

institute: University of Minnesota

summary: Our study aimed to investigate the biological impact of forebrain neuron-specific farnesyltransferase knockout in a transgenic APP/PS1 Alzheimer's disease model.

overall_design: We performed bulk mRNA-seq to examine the transcriptome changes associated with forebrain neuron-specific farnesyltransferase knockout in APP/PS1 mice. RNA-Seq data was collected from 6 mice (3 males & 3 female) from each genotype group (APP/PS1, APP/PS1/FTnKO, C57BL/6J WT) at 9-10 months of age. Sequencing was performed using Illumina NovaSeq 6000 platform, generating 20 million reads per sample on a 150-bp paired-end run.

first: Angela

last: Jeong